Gorin, Gennady and Pachter, Lior (2021) Direct simulation of a stochastically driven multi-step birth-death process. . (Unpublished) https://resolver.caltech.edu/CaltechAUTHORS:20210122-125501964
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Abstract
The description of transcription as a stochastic process provides a framework for the analysis of intrinsic and extrinsic noise in cells. To better understand the behaviors and possible extensions of existing models, we design an exact stochastic simulation algorithm for a multimolecular transcriptional system with an Ornstein-Uhlenbeck birth rate that is implemented via a special function-based time-stepping algorithm. We demonstrate that its joint copy-number distributions reduce to analytically well-studied cases in several limiting regimes, and suggest avenues for generalizations.
| Item Type: | Report or Paper (Discussion Paper) | |||||||||
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| Additional Information: | The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license. Version 1 - January 21, 2021; Version 2 - March 3, 2021. The DNA, pre-mRNA, and mature mRNA illustrations used in Figure 2, reproduced from [34], are derivatives of the DNA Twemoji by Twitter, Inc., used under CC-BY 4.0. G.G. and L.P. were partially funded by NIH U19MH114830. Code availability: MATLAB code that can be used to reproduce Figures 4-S3, including the simulation and plotting routines, is available at https://github.com/pachterlab/GP_2021. The authors have declared no competing interest. | |||||||||
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| DOI: | 10.1101/2021.01.20.427480 | |||||||||
| Record Number: | CaltechAUTHORS:20210122-125501964 | |||||||||
| Persistent URL: | https://resolver.caltech.edu/CaltechAUTHORS:20210122-125501964 | |||||||||
| Official Citation: | Direct simulation of a stochastically driven multi-step birth-death process. Gennady Gorin, Lior Pachter. bioRxiv 2021.01.20.427480; doi: https://doi.org/10.1101/2021.01.20.427480 | |||||||||
| Usage Policy: | No commercial reproduction, distribution, display or performance rights in this work are provided. | |||||||||
| ID Code: | 107661 | |||||||||
| Collection: | CaltechAUTHORS | |||||||||
| Deposited By: | Tony Diaz | |||||||||
| Deposited On: | 22 Jan 2021 21:19 | |||||||||
| Last Modified: | 16 Nov 2021 19:05 |
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